1HXS

CRYSTAL STRUCTURE OF MAHONEY STRAIN OF POLIOVIRUS AT 2.2A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution.

Miller, S.T.Hogle, J.M.Filman, D.J.

(2001) J Mol Biol 307: 499-512

  • DOI: https://doi.org/10.1006/jmbi.2001.4485
  • Primary Citation of Related Structures:  
    1HXS

  • PubMed Abstract: 

    A genetic algorithm-based computational method for the ab initio phasing of diffraction data from crystals of symmetric macromolecular structures, such as icosahedral viruses, has been implemented and applied to authentic data from the P1/Mahoney strain of poliovirus. Using only single-wavelength native diffraction data, the method is shown to be able to generate correct phases, and thus electron density, to 3.0 A resolution. Beginning with no advance knowledge of the shape of the virus and only approximate knowledge of its size, the method uses a genetic algorithm to determine coarse, low-resolution (here, 20.5 A) models of the virus that obey the known non-crystallographic symmetry (NCS) constraints. The best scoring of these models are subjected to refinement and NCS-averaging, with subsequent phase extension to high resolution (3.0 A). Initial difficulties in phase extension were overcome by measuring and including all low-resolution terms in the transform. With the low-resolution data included, the method was successful in generating essentially correct phases and electron density to 6.0 A in every one of ten trials from different models identified by the genetic algorithm. Retrospective analysis revealed that these correct high-resolution solutions converged from a range of significantly different low-resolution phase sets (average differences of 59.7 degrees below 24 A). This method represents an efficient way to determine phases for icosahedral viruses, and has the advantage of producing phases free from model bias. It is expected that the method can be extended to other protein systems with high NCS.


  • Organizational Affiliation

    Committee for Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GENOME POLYPROTEIN, COAT PROTEIN VP1A [auth 1]302Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GENOME POLYPROTEIN, COAT PROTEIN VP2B [auth 2]272Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GENOME POLYPROTEIN, COAT PROTEIN VP3C [auth 3]237Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
GENOME POLYPROTEIN, COAT PROTEIN VP4D [auth 4]68Human poliovirus 1 MahoneyMutation(s): 0 
UniProt
Find proteins for P03300 (Poliovirus type 1 (strain Mahoney))
Explore P03300 
Go to UniProtKB:  P03300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03300
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download Ideal Coordinates CCD File 
E [auth 1]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
MYR
Query on MYR

Download Ideal Coordinates CCD File 
F [auth 4]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Work: 0.268 
  • R-Value Observed: 0.268 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 320.5α = 90
b = 355.25β = 90
c = 377.25γ = 90
Software Package:
Software NamePurpose
DJFmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
DJFphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 2.0: 2023-04-19
    Type: Remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 2.1: 2023-09-20
    Changes: Data collection, Refinement description